[gmx-users] Periodic saving of checkpoint file

[Nicolas Cheron]

Hi Mark,

Thank you for your answer. I didn't know this option. From what I have
read, eneconv is for reading parameters for Nose-Hoover or
Parrinello-Rahman coupling. Thus, if I am doing first an NVT simulation
with the velocity-rescale thermostat or a Langevin dynamics, I don't need
the .edr file, right ? Can you please confirm that this is enough to
prepare the tpr from the time 50ps of the NVT simulation:

gmx grompp -v -f NVE.mdp -n Index.ndx -o NVE.tpr -c NVT.gro -t NVT.trr
-time 50 -p Protein.top -po NVE_mdout.mdp

Thank you


Le lun. 5 nov. 2018 à 17:50, Mark Abraham <mark.j.abraham at gmail.com> a
écrit :

> Hi,
>
> Since you are anyway intending to change the ensemble, you can just use
> nstxout, nstvout and nstenergy to write output every 10ps. That content is
> equivalent to that of the checkpoint. Use trjconv and eneconv afterwards to
> split those up, and use them as inputs to grompp -e -t along with the
> regular inputs.
>
> Mark
>
> On Mon, Nov 5, 2018 at 5:14 PM Nicolas Cheron <
> nicolas.cheron.boulot at gmail.com> wrote:
>
> > Dear all,
> >
> > I would like to run a long NVT simulation and save a checkpoint file
> every
> > 10ps (in order to then run short NVE simulations from each checkpoint).
> Is
> > there a way to save a .cpt file every 10ps in an automatic way?
> >
> > I can do it with other program, for example with Amber "ntwr=-5000" will
> > save a new restart file every 5000 steps. For now with Gromacs, the only
> > thing I have found is to write a loop where at each step I extend the
> > simulation time of 10ps with convert-tpr, perform the 10ps simulation,
> save
> > the .cpt, and then loop again.
> >
> > Thanks for your help.
> >
> > Nicolas
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